Extended Data Fig. 2: XLMS-driven structural modelling of TCRC.

Supplementary to Fig. 2. a–d, Reconstitution of the TCRC without nucleic acids. a, Isolation of the RNAP–NusA–UvrABD complex by SEC. SDS-Coomassie gel represents the protein fraction eluted from the main peak (P). b, DLS analysis of the RNAP–NusA–UvrABD complex. The ‘P’ fraction from a was subjected to DLS. Raleigh sphere (R) estimate of the complex molecular weight (MW = 908 kDa), which deviates by only 1.7% from the theoretical MW of a uniform monodispersed complex containing 1 RNAP, 1 NusA, 2 UvrD, 2 UvrA, and 1 UvrB molecules. c, Network view of the highly confident non-redundant inter-protein cross-links (Supplementary Table 1). d, XLMS-based model of the reconstituted RNAP:NusA:UvrABD complex. The model was built based on the in vitro cross-links using PatchDock and the workflow described in Extended Data Fig. 11 and Methods. e–h, Mapping UvrD-EC interactions in vitro. e, Isolation of the EC:NusA:UvrD complex by SEC. SDS-Coomassie gel represents the protein fraction eluted from the main SEC peak (P). f, DLS analysis of the EC:NusA:UvrD complex. “P” fraction from (e) was subjected to DLS. Raleigh sphere (R) estimate of the complex molecular weight (MW = 620 kDa), which deviates by only 2% from the theoretical MW of a uniform monodispersed complex containing 1 RNAP, 1 NusA, and 2 UvrD molecules. g, Network view of the highly confident non-redundant inter-protein cross-links between RNAP subunits, NusA, and UvrD (Supplementary Table 1). h, XLMS-based model of the RNAP:NusA:UvrD complex (Extended Data Fig. 11 and Methods). The model shows the positioning of UvrD monomers relative to the transcription bubble. Blue star indicates the DNA-UvrD cross-link previously mapped in the EC¹⁸. CTD of UvrD2 is shown by green hexagon. RNA is not shown.